title: Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding.
abstract: Fluorescence resonance energy transfer is a powerful technique which is often used to probe the properties of proteins and complex macromolecules. The technique relies on relatively large fluorescent dyes which are engineered into the molecule of interest. In the case of small proteins, these dyes may affect the stability of the protein, and modify the folding kinetics and the folding mechanisms which are being probed. Here we use atomistic simulation to investigate the effect that commonly used fluorescent dyes have on the folding of a four-helix bundle protein. We show that, depending on where the dyes are attached, their effect on the kinetic and thermodynamic properties of the protein may be significant. We find that, while the overall folding mechanism is not affected by the dyes, they can destabilize, or even stabilize, intermediate states.
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: Lucy R
authors.initials: LR
authors.lastname: Allen
authors.forename: Emanuele
authors.initials: E
authors.lastname: Paci
mesh_terms: D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D005456:Fluorescent Dyes / Q000737:chemistry / Q000494:pharmacology*; D007700:Kinetics; D008958:Models, Molecular; D008962:Models, Theoretical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D005456:Fluorescent Dyes; D010455:Peptides; D011506:Proteins